BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240253.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 621,888 number of mapped reads = 450,679 (72.47%) number of supplementary alignments = 2,592 (0.42%) number of secondary alignments = 0 number of mapped bases = 29,086,002 bp number of sequenced bases = 29,068,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,444 duplication rate = 7.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9281 >>>>>>> ACTG content number of A's = 8,306,160 bp (28.57%) number of C's = 5,235,524 bp (18.01%) number of T's = 9,080,576 bp (31.24%) number of G's = 6,431,043 bp (22.12%) number of N's = 15,427 bp (0.05%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 308,590 number of insertions = 2,315 mapped reads with insertion percentage = 0.51% number of deletions = 9,733 mapped reads with deletion percentage = 2.13% homopolymer indels = 49% >>>>>>> Coverage mean coverageData = 0.0094X std coverageData = 0.2045X There is a 0.56% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2002626 0.008034587805500393 0.22047689171476004 chr2 243199373 2683062 0.011032355745423736 0.21197333087103445 chr3 198022430 1834758 0.009265404934178417 0.17757237599861375 chr4 191154276 1889777 0.009886135113189934 0.18406255849255473 chr5 180915260 1812460 0.010018281487144865 0.191378619453073 chr6 171115067 1726155 0.010087685615668198 0.19301384100021426 chr7 159138663 1734852 0.010901511721259088 0.2345790179540415 chr8 146364022 1635830 0.011176448813356605 0.3839387441143945 chr9 141213431 1061329 0.007515779430357443 0.1678763019179273 chr10 135534747 1542573 0.011381383992991849 0.21057975148407304 chr11 135006516 1236673 0.009160098613314339 0.19051239985605412 chr12 133851895 1304054 0.009742514291635543 0.18174531052483123 chr13 115169878 943082 0.008188616818713657 0.17870048612001252 chr14 107349540 958324 0.008927136529881731 0.1765912961270738 chr15 102531392 795027 0.00775398621331504 0.16424444474576208 chr16 90354753 911380 0.01008668575520316 0.18099523434349252 chr17 81195210 672392 0.008281178163096075 0.15107621238303992 chr18 78077248 660722 0.008462414044101554 0.20926063207450035 chr19 59128983 471372 0.00797192808136071 0.1708109558092201 chr20 63025520 550388 0.00873277999134319 0.16147025017697278 chr21 48129895 441025 0.009163223813390825 0.1740541641689952 chr22 51304566 324876 0.006332301885177237 0.14878438609332903 chrMT 16571 4611 0.278257196306801 0.6818008496361934 chrX 155270560 1805525 0.011628250712820254 0.21019254048766678 chrY 59373566 83129 0.00140010118307531 0.05888720106023564